Rhizopus stolonifer (black bread mold) is a widely distributed thread-like Mucoralean mold. Commonly found on bread surfaces, it takes food and nutrients from the bread and causes damage to the surface where it lives.

Asexual spores are formed within pinhead-like sporangia, which break to release the spores when mature. Germination of these spores forms the haploid hyphae of a new mycelium. R. stolonifer grows rapidly at temperatures between 15 and 30°C.

Rhizopus stolonifer is a heterothallic species (Schipper 1984), in that sexual reproduction happens only when opposite mating types (designated + and -) come in contact. Successful mating results in the formation of durable zygospores at the point of contact. Subsequently, the zygospore germinates and forms a sporangiophore whose sporangium contains both + and - haploid spores. There are two varieties: R. stolonifer var. stolonifer produces straight, erect sporangiophores, whereas those of R. stolonifer var. lyococcos are curved. A closely related species, Rhizopus sexualis, differs primarily in being homothallic (self-compatible).

Molds (or moulds; see spelling differences) are fungi that grow in the form of multicellular filaments called hyphae. A connected network of these tubular branching hyphae has multiple, genetically identical nuclei and is considered a single organism, referred to as a colony. In contrast, fungi that grow as single cells are called yeasts.

Molds are considered to be microbes and do not form a specific taxonomic or phylogenetic grouping, but can be found in the divisions Zygomycota, Deuteromycota and Ascomycota. Some molds cause disease or food spoilage; others play an important role in biodegradation or in the production of various foods, beverages, antibiotics and enzymes.

There are thousands of known species of molds which include opportunistic pathogens, saprotrophs, aquatic species and thermophiles. Like all fungi, molds derive energy not through photosynthesis but from the organic matter in which they live. Typically, molds secrete hydrolytic enzymes, mainly from the hyphal tips. These enzymes degrade complex biopolymers such as starch, cellulose and lignin into simpler substances which can be absorbed by the hyphae. In this way molds play a major role in causing decomposition of organic material, enabling the recycling of nutrients throughout ecosystems. Many molds also secrete mycotoxins which, together with hydrolytic enzymes, inhibit the growth of competing microorganisms.

Rye bread is a type of bread made with various percentages of flour from rye grain. It can be light or dark in color, depending on the type of flour used and the addition of coloring agents, and is typically denser than bread made from wheat flour. It is higher in fiber than white bread and is often darker in color and stronger in flavor. Rye bread has notable health benefits when compared to white bread.

While rye and wheat are genetically close enough to interbreed (the resulting hybrids are known as triticale), there are some substantial differences in the biochemistry of wheat and rye that can drastically affect the breadmaking process. A key issue is amylases – while wheat amylases are generally not heat-stable and have no effect on the stronger wheat gluten, rye amylase remains active at substantially higher temperatures. Since rye gluten is not particularly strong, the main structure of the bread is based on complex polysaccharides, including rye starch and pentosans, and the amylases in the flour can break down the resulting structure, inhibiting the rise of the dough.